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- EMDB-44442: Dimeric form of LDL, LDL receptor and Legobody -

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Basic information

Entry
Database: EMDB / ID: EMD-44442
TitleDimeric form of LDL, LDL receptor and Legobody
Map data
Sample
  • Complex: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
    • Complex: Apolipoprotein B 100
    • Complex: Low-density lipoprotein receptor
    • Complex: Legobody Fab
    • Complex: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion
KeywordsApolipoprotein B 100 / ApoB 100 / LDL / LDL receptor / LIPID TRANSPORT
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsDearborn AD / Reimund M / Graziano G / Lei H / Kumar A / Neufeld EB / Remaley AT / Marcotrigiano J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2025
Title: Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor.
Authors: Mart Reimund / Altaira D Dearborn / Giorgio Graziano / Haotian Lei / Anthony M Ciancone / Ashish Kumar / Ronald Holewinski / Edward B Neufeld / Francis J O'Reilly / Alan T Remaley / Joseph Marcotrigiano /
Abstract: Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial ...Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial hypercholesterolaemia, an autosomal dominant disease that is characterized by a marked increase in LDL cholesterol (LDL-C) and a higher risk of cardiovascular disease. The structure of apoB100 on LDL and its interaction with LDLR are poorly understood. Here we present the cryo-electron microscopy structures of apoB100 on LDL bound to the LDLR and a nanobody complex, which can form a C-symmetric, higher-order complex. Using local refinement, we determined high-resolution structures of the interfaces between apoB100 and LDLR. One binding interface is formed between several small-ligand-binding modules of LDLR and a series of basic patches that are scattered along a β-belt formed by apoB100, encircling LDL. The other binding interface is formed between the β-propeller domain of LDLR and the N-terminal domain of apoB100. Our results reveal how both interfaces are involved in LDL dimer formation, and how LDLR cycles between LDL- and self-bound conformations. In addition, known mutations in either apoB100 or LDLR, associated with high levels of LDL-C, are located at the LDL-LDLR interface.
History
DepositionApr 10, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44442.png

Downloads & links

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Map

FileDownload / File: emd_44442.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 512 pix.
= 849.92 Å		1.66 Å/pix.
x 512 pix.
= 849.92 Å		1.66 Å/pix.
x 512 pix.
= 849.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16318023 - 0.41963625
Average (Standard dev.)-0.00040699824 (±0.020268986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 849.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map b

Fileemd_44442_half_map_1.map
AnnotationHalf map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map a

Fileemd_44442_half_map_2.map
AnnotationHalf Map a
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apolipoprotein B 100 on LDL with LDL receptor and Legobody

EntireName: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
Components
  • Complex: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
    • Complex: Apolipoprotein B 100
    • Complex: Low-density lipoprotein receptor
    • Complex: Legobody Fab
    • Complex: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion

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Supramolecule #1: Apolipoprotein B 100 on LDL with LDL receptor and Legobody

SupramoleculeName: Apolipoprotein B 100 on LDL with LDL receptor and Legobody
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Apolipoprotein B 100

SupramoleculeName: Apolipoprotein B 100 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Low-density lipoprotein receptor

SupramoleculeName: Low-density lipoprotein receptor / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Legobody Fab

SupramoleculeName: Legobody Fab / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #5: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion

SupramoleculeName: Legobody MBP/IgG-binding protein A/IgG-binding protein G Fusion
type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 51.38 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3689076 / Details: Topaz particle picking
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234099
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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